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Shortly after graduating from the American Film Institute, Coto wrote and directed an episode of Tales from the Crypt. He went on to write and direct the feature films Dr. Giggles and Star Kid. He was a writer and producer on the recent incarnation of The Outer Limits, and also created the short-lived science fiction series Odyssey 5 for Showtime, whose cast included Tamara Craig Thomas, Leslie Silva, and Peter Weller, the latter two of which Coto worked with again on Enterprise. (Coto subsequently cast Weller again on other series – see below.)

Coto was brought into Star Trek for the third season of Star Trek: Enterprise and wrote several episodes. Showrunners Rick Berman and Brannon Braga were so impressed with his work, and his love for the original Star Trek, that he became the new executive producer for the fourth and final season.

His influence helped the show fulfill its initial purpose, a prequel to the beloved Original Series and Star Trek: The Next Generation, through a series of episodes, many of them parts of two- or three-part arcs, that explored some of the missing links in the Trek mythology. Episodes focused on what became of the Augments between the Eugenics Wars and the return of Khan, why the Vulcans changed between Enterprise and TOS, why the Klingons of TOS look different from those in other appearances, how the threat of the Romulans helped to birth the Federation, and who created the transporter. Other homages to earlier Trek incarnations include the appearance of a TOS-era Constitution-class ship and the Enterprise crew donning original series uniforms, as well as a guest appearance by Next Generation cast member Brent Spiner.

After an eighth and final season of 24 (featuring Nazneen Contractor), Coto became an executive producer on the Showtime series Dexter, where he yet again worked with Peter Weller, as well as Raphael Sbarge.

In the Star Trek: Legacy video game, the player encounters a Poseidon-class destroyer called USS Coto in the first mission of the Star Trek: Enterprise-era campaign. It is likely that the one of the game's producers or programmer named the vessel in honor of Coto's work on the series.